Transposons and the Dynamic Genome (eBook)

Preface 6
Contents 14
Theoretical Approaches to the Dynamics of Transposable Elements in Genomes, Populations, and Species 17
1 Introduction 17
2 Genome Colonization 18
3 TE – Genome Coevolution 25
4 Conclusion 29
References 30
Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements 36
1 Introduction 36
2 Lessons from the Past 38
3 Towards an Understanding of TE Regulation. From Sequence to Epigenetics 42
4 Conclusion 50
References 52
Morphological Characters from the Genome: SINE Insertion Polymorphism and Phylogenies 59
1 On the Importance of Getting the Phylogeny Right 59
2 SINEs 61
3 SINE Insertion Polymorphisms as Characters for Phylogeny 62
4 Methods 73
5 Conclusion 79
References 80
Genome Defense Against Transposable Elements and the Origins of Regulatory RNA 90
1 The Ascent of Regulatory RNA 90
2 RNAi and Genome Defense 92
3 TEs and microRNAs 94
4 Repeat-Associated Sequences and piRNAs 96
5 Transcript Infection Model 101
References 103
When Drosophila Meets Retrovirology: The gypsy Case 108
1 Introduction 108
2 Historical Background 110
3 Finding the Road to the Germline 111
4 Origin of the gypsy Env 112
5 Structural Analysis of gypsy Env 115
6 Functional Analysis of gypsy Env 116
7 Role of gypsy Env 116
8 Conclusion 117
References 118
Transposon–Host Cell Interactions in the Regulation of Sleeping Beauty Transposition 121
1 Introduction 122
2 The Sleeping Beauty Transposable Element: Structure and Mechanism of Transposition 122
3 Regulation of Transposition 123
4 Concluding Remarks 136
References 136
Interactions of Transposons with the Cellular DNA RepairMachinery 145
1 Introduction 146
2 The Types of DNA Damage Produced by Transposons 146
3 Cellular Processes Potentially Involved in Signaling and Repairing Transposition Intermediates 147
4 The Main Classes of Transposons 152
5 Repetitive Elements and Genome Stability 173
6 Transposition and Cell Cycle 175
7 Concluding Remarks 177
References 178
Subject Index 189